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Open Access Research article

Development-dependent changes in the tight DNA-protein complexes of barley on chromosome and gene level

Tatjana Sjakste1*, Kristina Bielskiene2, Marion Röder3, Olga Sugoka1, Danute Labeikyte2, Lida Bagdoniene2, Benediktas Juodka2, Yegor Vassetzky4 and Nikolajs Sjakste5

Author Affiliations

1 Genomics and Bioinformatics, Institute of Biology, University of Latvia, Miera 3, LV2169 Salaspils, Latvia

2 Department of Biochemistry and Biophysics, Vilnius University, M. K. Čiurlionio 21, LT2009 Vilnius, Lithuania

3 Gene and Genome Mapping, Leibniz Institute of Plant Genetics and Crop Plant Research, Correnstrasse 3, 06466, Gatersleben, Germany

4 UMR-8126, Institut Gustave Roussy, 39, rue Camille-Desmoulins, 94805 Villejuif, France

5 Faculty of Medicine, University of Latvia, Šarlotes 1a, LV1001, Riga, Latvia

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BMC Plant Biology 2009, 9:56  doi:10.1186/1471-2229-9-56

Published: 12 May 2009

Abstract

Background

The tightly bound to DNA proteins (TBPs) is a protein group that remains attached to DNA with covalent or non-covalent bonds after its deproteinisation. The functional role of this group is as yet not completely understood. The main goal of this study was to evaluate tissue specific changes in the TBP distribution in barley genes and chromosomes in different phases of shoot and seed development. We have: 1. investigated the TBP distribution along Amy32b and Bmy1 genes encoding low pI α-amylase A and endosperm specific β-amylase correspondingly using oligonucleotide DNA arrays; 2. characterized the polypeptide spectrum of TBP and proteins with affinity to TBP-associated DNA; 3. localized the distribution of DNA complexes with TBP (TBP-DNA) on barley 1H and 7H chromosomes using mapped markers; 4. compared the chromosomal distribution of TBP-DNA complexes to the distribution of the nuclear matrix attachment sites.

Results

In the Amy32b gene transition from watery ripe to the milky ripeness stage of seed development was followed by the decrease of TBP binding along the whole gene, especially in the promoter region and intron II. Expression of the Bmy1 gene coupled to ripening was followed by release of the exon III and intron III sequences from complexes with TBPs. Marker analysis revealed changes in the association of chromosome 1H and 7H sites with TBPs between first leaf and coleoptile and at Zadoks 07 and Zadoks 10 stages of barley shoot development. Tight DNA-protein complexes of the nuclear matrix and those detected by NPC-chromatography were revealed as also involved in tissue- and development-dependent transitions, however, in sites different from TBP-DNA interactions. The spectrum of TBPs appeared to be organ and developmental-stage specific. Development of the first leaf and root system (from Zadoks 07 to Zadoks 10 stage) was shown as followed by a drastic increase in the TBP number in contrast to coleoptile, where the TBPs spectrum became poor during senescence. It was demonstrated that a nuclear protein of low molecular weight similar to the described TBPs possessed a high affinity to the DNA involved in TBP-DNA complexes.

Conclusion

Plant development is followed by redistribution of TBP along individual genes and chromosomes.